The Forgotten
by Noien-sama
Summary: Summary: Naruto is betrayed by the village. Kidnapped, tortured and experimented on Naruto wonders if he'll ever see daylight again.
1. Chapter 1

N: Rewrite of "The Forgotten". Please enjoy.

Summary: Naruto is betrayed by the village. Kidnapped, tortured and experimented on Naruto wonders if he'll ever see daylight again.

Warnings: AU, yaoi, violence/gore, hurt/comfort, cursing, M/M sex scenes and m-preg.

Disclaimer: I don't own Naruto.

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><p>Chapter One: Failure<p>

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><p>It turns out pushing his already heavily depleted chakra towards his seal was a very painful thing to do when you've just had a hand powered by an electric justu thrust through your abdomen. But he had to. He had failed his mission and he deserved this for it.<p>

"**stop resisting me boy."** Kyuubi growled darkly from the recesses of his mind pushing back angrily at the chakra defense. Naruto struggled to contain the gasp of agony feeling the pain from his belly traveling hotly through his body at an alarming rate.

It hurt. He hurt so badly but he would not let Kyuubi help him. He deserved every aching moment of this pain. He had failed to do as he promised breaking several of his nindos' in the process.

He failed to save Sasuke from Orochimaru. He failed to save Sakura's love for her. What kind of friend was he to let this happen? To let them all fall apart and be broken?

He should have seen the path where Sasuke was heading down the moment he saw that look in his eyes at the hospital. Heck, he should have seen it before when Sasuke spoke about avenging his family. But he was so weak. Even when he was backed by the Kyuubi he was still too weak to bring back his friend.

"god…" Naruto rasped out sobbing. Sasuke was his friend. He was the only one that Naruto could confidently say was his friend without an instant denial from the other or a hateful glare.

And now he was gone, leaving the village and his friends behind to be embraced by the darkness that is taking over his heart and to be forever in the clutches of the sannin that already took so much from Naruto.

Sobs tore from his throat harshly making him curl up to minimize the jostling of his wounds from the force of his tears. Sorrow washed over him like the lake water still falling from the sky, drenching him in its cold grip.

He should die like this, alone and in the cold.

Kyuubi rumbled as he processed Naruto's self-deprecating thoughts flowing across his mind as they were his own. He was more than aware of the life Naruto led up to this point and was not surprised by the reaction he was having by the friend's betrayal.

The blonde felt as though he was the very demon he held in his body and so felt actions brought against him by those he cared for was warranted by that thought alone.

"_**Like today"**_ Kyuubi thought barking out a short humorless laugh. What a pathetic being Uchiha Sasuke was using others to gain power for feeble and idiotic gains. That boy had no idea what it means to have power. Burning irreplaceable bridges would get him nowhere.

Smirking to himself Kyuubi broke through Naruto's chakra's defensives and started to heal the now unconscious boy.

**Outside Naruto's Mind**

"Is that it?" a young man spoke staring down at Naruto's fallen body unimpressed. The second adolescent accompanying the first gave a stiff smile as he answered.

"yes."

"It's wounded. Do you suppose Danzo-sama will be displeased?" The first man asked poking Naruto in his side gently with his foot. Naruto winced at the pressure but otherwise stayed unconscious.

"No. The demon will keep its vessel alive." The second answered again, still smiling. The first man turned to the other with a blank look.

"Fine, you carry it then. I don't want it touching me."

"He can't technically touch you if he's unconscious." The second said blandly. The first hissed at him but otherwise did nothing but storm away from the aggravating man. The second man watched him go briefly before bending down to pick up Naruto, easily cradling the smaller form in his arms. Staring at the tear stained face he wondered how long this boy would last under his master's grasp.

Somehow he doubted it'll be long.

"Let's get you to your new home, yes?"

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><p>"Danzo-sama Patient X has arrived to Laboratory 8 as scheduled but I am afraid Uchiha Sasuke was not with them." A plain looking woman dressed primly in nurses uniform reported quickly as tried to keep up with her master's long strides. The man adorned in bandages glanced at her with his visible eye and nodded feeling pleased.<p>

It didn't matter if they hadn't got the youngest Uchiha in their grasp, he was only meant to be a backup plan anyway. Since his root was able to acquire the originals samples Sasuke's lesser genes weren't necessary for the experiment.

"No matter. Tell me of the patient's state." Danzo ordered slowing his steps as they neared their destination. The woman flipped a few pages on her clipboard before answering.

"He was wounded but the Kyuubi healed him before he could die. As per your orders I have told the doctors to proceed with the surgery."

"Good. And what of the girl?"

"we chose the very best candidate for the experiment."

"how old?"

"15 years."

" Wonderful, it will fit well in his body."

"Yes, after the removal of any unnecessary organs it will be a clean fit."

"The seals?"

"Already in place. Kyuubi will not be able to interfere."

"hmm." Danzo murmured pleased. Coming to a stop to an open door the pair walked inside to be greeted by a close view of the very surgery they were discussing. Danzo took his seat near the front leaving the woman to stand behind awaited further orders. Danzo ignored her in favor of watching Naruto's now naked form be placed on the metal operating table.

He watched Naruto's small rounded face whilst the doctors and nurses filling the room worked to prepare for the surgery. He loved the innocence still so strongly embedded in that pretty face.

He was going to enjoy tearing that away.

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><p>N: this is going to be longer than the original and will be the plot holes I've left in the last one. But I hoped you enjoyed this first chapter and please leave a review.<p> 


	2. Chapter 2

N:second chapter.

Summary: Naruto is betrayed by the village. Kidnapped, tortured and experimented on Naruto wonders if he'll ever see daylight again.

Warnings: AU, yaoi, violence/gore, hurt/comfort, cursing, M/M sex scenes and m-preg.

Disclaimer: I don't own Naruto.

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><p>Chapter Two: Aware<p>

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><p>The first thing Naruto took notice of as he slowly came back to the world was the too bright lighting being blasted into his eyes. Instincts made him want to turn his head away from the painful light but he soon found out he couldn't. He tried to move his arms but they weren't responding to his demands. Nothing was.<p>

His eyes gradually adjusted to the light and looking franticly he spotted people in white hovering over him speaking in distorted voices and shuffling around him uneasily. He guessed they were doctors and nurses from what features he could make out. He noticed all of them wore masks like you would wear if you were… Eyes widening in panic as dread and fear settled deep within him once he realized what was happening to him.

He was in surgery and he was awake.

He tried to scream in protest and in fear but his mouth stay unmoving. He wanted to thrash about to get away but his body was still. He blinked rapidly as he felt a pressure on his abdomen under his navel and he knew what was to come.

The pressure slid down from his navel to just to the top of his pelvis. Tear leaked from his eyes at the horror of what was happening. He could do nothing to stop it.

He was immobile and paralyzed to a point of numbness but due to his metabolic speed whatever anesthesia they gave him wore off quicker than normal. So he was stuck unable to move while these unknown people cut into him. Naruto lay there for hours on end as they cut into him, removed organs, put things inside of him and take things away.

He could feel no pain but he could feel the fingers of doctors shifting organs within him, feel the pressure of the scalpels they used. The padding of sponges and the laughter from the nurses as they peeked inside him amazed that he looked so much like them.

It made Naruto sick. It was only by the grace of Kami that Kyuubi decided to bring him back under.

Danzo watched as Naruto's eyes fluttered closed and he almost slumped in disappointment. He was surprised at first when Naruto opened his eyes at the very beginning of the surgery and was amused that he remained awake during the majority of it.

It was an interesting show in what he expected to be a boring surgery. The boy eyes looked so frightened at the first cut Danzo wondered just how much he could feel.

Seeing as he couldn't move, Danzo doubted he could feel too much. No matter though, the boy was in for much worse once he had his hands on him. Just thinking of that creamy tanned flesh made him want to forgo his plans and put his own seed in that body. But alas he had to look at the big picture at hand.

"Is everything in place with the council?" he asked his nurse. She took her eyes off of the surgery to face him before she answered.

"Yes sir, they are eagerly awaiting your results."

"Of course. Is the specimen ready for transfer?"

"Yes sir, on ice and awaiting your order." She replied softly.

"Good, good. Have Sai escort the vessel to his new home and then send him to my office."

"Yes sir." Danzo looked back on Naruto briefly before rising from his seat. He wanted to stay longer but no doubt Tsunade will have gotten word by now that her little pet was missing and he had to do a little preemptive damage control before she decided to come sniffing around. He hated that loud mouthed big breasted woman with his very being. If it weren't for her medical prowess he doubted anyone would miss her if he killed her.

But again, it was no matter. It was necessary for now to be on her good side to avoid too much suspicion on his person. Looking to his head nurse he addressed her once more.

"I expect you to keep me informed while I go play nice?"

"Yes sir, of course sir."

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><p>Tsunade sighed heavily as she finally was able to sink into her chair after stabilizing Neji. She couldn't believe the day she had to endure. Very few words can describe what she was feeling at this moment.<p>

People can say she was angry. But, no she was _livid._

First her snake bastard of a teammate snuck in her village and killed her beloved sensei in cold blood. Then he no doubt plied that weak willed brat with promises of power and skills to kill his brother, knowing full well of the danger and damage it can cause.

It made her furious to think about it as the seconds ticked by and Naruto still wasn't under her care.

How dare he and that little bastard Uchiha brat come and fuck up what little good she managed to acquire in this village she so dearly wanted to forget and leave behind.

How fucking dare they!

If her old teammate wasn't a perverted psychopath with an obsession with immortality and the Uchiha brat wasn't so stupidly trying to obtain power to kill his brother her grandson wouldn't be after his sorry ass.

And he wouldn't have been hurt or gone missing.

She swore with every fiber of her being she was going to find her grandson, tuck him away for a few months while she hunted down her teammate killed him and took that damn Uchiha brat back to village.

Then she'd sit back and let the council have his spoiled ass. Then she'd take a much deserved vacation and spend some time with the child she'd come to adore.

A knock on her door brought her out of her bloody musings and with a hard glare she yelled for whomever to come in. She wondered who would dare knock on her door after she gave the exclusive order for no visitors unless it was directly connected to Naruto. This better be Kakashi with good news or she was going to start killing.

When the doors opened fully to reveal her visitor she fought not to glare hatefully at the man standing before her. Danzo.

"What?" she ground out sneering slightly at the bandaged man. Danzo held her look coldly stepping fully into her office and taking a seat without her offering him one. Giving her a decidedly friendly look he began his offer.

"I see you are of need of some assistance."

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><p>N:I hoped you enjoyed the second chapter!<p> 


	3. Chapter 3

N:Thank you all for all your wonderful reviews. And this chapter should clear up any misunderstanding anybody might have from the last chapter.

Summary: Naruto is betrayed by the village. Kidnapped, tortured and experimented on Naruto wonders if he'll ever see daylight again.

Warnings: AU, yaoi, violence/gore, hurt/comfort, cursing, M/M sex scenes and m-preg.

Disclaimer: I don't own Naruto.

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><p>Chapter Three: The proposal<p>

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><p>Tsunade sunk heavily in her seat feeling the full weight of her age for the first time in years. Danzo had just left her office not a moment ago and what transpired made her want to guzzle down her whole supply of sake just to draw her mind away from the deal she just made with the creepy man.<p>

But what else she could do? The nin under her control had no qualms about leaving her precious grandson wherever he may be so that made them unable to carry out the search and rescue mission for him. For that reason alone that made her agree to Danzo proposal.

**10 minutes ago**

"_I see you are in need of some assistance." Danzo began carefully watching her face. Tsunade narrowed her eyes at him leaning back in her chair and folding her arms under her chest._

"_And if I am? What is your interest, Danzo?" _

"_I can provide you with an impartial party to accompany a team of your choosing to find Uzamaki-san." Danzo spoke slowly and clearly remembering to address Naruto by his name lest he anger the lady Hokage._

"_Oh? One of your ROOT? Why should I risk one of your minions finding my Naruto just for you to begin some twisted plan concerning Naruto?" Tsunade said glaring and Danzo resisted the urge to smirk at her statement. She had no idea how right she was._

"_You'd just have to put up with that fear if you ever what to successfully find him. You know the residents of our lovely village are inclined to look the other way concerning Uzamaki's disappearance." Tsunade frowned and reluctantly nodded agreeing with him._

"_But what is you intention? I know you are in the same mindset as the villagers." Danzo gave her a cool look before answering._

"_Power of course." Tsunade jerked in surprise at his statement making Danzo hurry and explain._

"_If any other village find Uzamaki-san and discover his occupant we would be at a serious disadvantage" Tsunade stared at him long and hard and just when he thought his plan just might go through she nodded._

"_Okay. send me your ROOT member to me tomorrow and we'll go from there." Danzo smiled feeling pleased beyond words and he stood ready to leave. Moments before he reached the door Tsunade spoke once more._

"_Be wary Danzo. If anything happens to Naruto because of you, I'll tear you apart." He turned to face her with a chilly smile._

"_Of course, my Lady."_

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><p>Taking out her hidden stash of sake Tsunade dismissed the cup and grabbed the jug opening it quickly and drank straight from the jug. It was gone in a matter of moments and she reeled from the slight burn. A tear escaped her eye and she quickly snatched another jug from her drawer.<p>

Her worry settled in her stomach alongside the sake and she continued to try and drown it with the alcohol.

She just hoped that she made the right decision.

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><p>Naruto sniffed wetly as he clung to Kyuubi's muzzle, shaking slightly at the pains that ran rapid though him. Kyuubi wrapped him in the healing warmth of his chakra but even with his comforting embrace Naruto could not stop crying. He felt ill at every thought that sprang up in his mind, reliving every detail of that horrible surgery.<p>

Since he could not wake up at the moment he asked Kyuubi to tell him what was done to his body even though Naruto was so afraid of what he would hear considering where his pain was felt most heavily. After great hesitation the fox relayed what he could.

He told Naruto that they took out what made him internally male and replaced it with a uterus from a female. He told him that a uterus is the organ that made having babies possible and then he said they removed his testacies and made a faux vagina using the skin of his still underdeveloped testis.

And then Kyuubi explained to him the reasons behind the actions of what the people who captured him. For some unknown agenda they wanted Naruto to be able to bear children and that is why they made him partly female. Kyuubi said that they expected him to heal him completely and make sure every part of him including his newly added pieces was functioning accurately.

They expected it because they thought that he'd be at least selfish enough to keep his host healthy. Then Kyuubi told him gently that soon he'd be producing eggs of his own and with the help of Kyuubi he'd have a chakra womb to carry a baby in when and if they put a seed in him.

When Kyuubi finished Naruto was already bent over and crying his eyes out. He came to one clear cut conclusion to Kyuubi's words. He was a freak! The reality of the fact that he wasn't a true boy anymore struck his heart in more ways than one.

One of the few things that made him somewhat normal was gone and he didn't know what to do. How could he deal with this? And he couldn't even think about the baby part of the equation.

"Ah!" pain attacked him suddenly making him curl into himself from the force of it. Nausea washed over him. Naruto struggled to keep the bile from spewing forth. Dizziness fogged his mind; harsh cold shakes raked his small form.

Kyuubi growled angrily; sensing someone's presence over Naruto's sleeping body. Vaguely he could feel a sight pinch on Naruto's arm and immediately reacted. Sending chakra through Naruto's veins to burn whatever those disgusting humans were injecting into his kit.

**Outside Naruto's Mind**

A nurse stared at the body of Patient X and sneered at the boy's face. It was unfair that someone;no something so evil could have a face like that. Coloring like his was a rarity in the village. Paired with that skin tone, she was sure if he weren't holding that being inside him he'd be heartbreaker.

It was no wonder why her superior Danzo wanted the boy. She supposed the demon looked that way to distract humans from it's nature. Feeling a twinge of envy the nurse decided it was time for him to wake up. The little monster didn't deserve to hide away from the pain.

Reaching into her pocket she pulled out a syringe full of a drug that would counteract against the antithsea keeping him asleep. Grabbing a thin arm closest to her she quickly administered the drug. Her green eyes narrowed in malicious glee as Naruto began to awake; trembling as the full brunt of his pain crashed over him.

The nurse gave a nasty little smile to Naruto; pulling her arm back slightly to pull the needle from his arm. She did it a second to late as Kyuubi's chakra found the source of Naruto new pain. She barely had time to scream as the syringe flew from Naruto's arm and embedded itself into her eye.

Howling in pain, she threw herself away as to avoid anymore flying weapons. A root member assigned to watch over Naruto room stared at the thrashing and crying woman impassively before signaling a passing nurse to get help. He himself stayed rooted to his post and made no move to help the woman.

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><p>N: sorry for the late update. You would believe the trouble I went through to upload this chapter. My new place has no wifi. And I have no keyboard. You guys are lucky that I'm an artist and have in invested in a pen tablet. Anyhoo shout out to Flightless Bird. Thanks for your awesome review.<p> 


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